Subsurface microbial oxidation of overridden soils and vegetation beneath glaciers and ice sheets may affect global carbon budgets on glacial–interglacial timescales. The likelihood and magnitude of this process depends on the chemical nature and reactivity of the subglacial organic carbon stores. We examined the composition of carbon pools associated with different regions of the Greenland ice sheet (subglacial, supraglacial, proglacial) in order to elucidate the type of dissolved organic matter (DOM) present in the subglacial discharge over a melt season. Electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry coupled to multivariate statistics permitted unprecedented molecular level characterization of this material and revealed that carbon pools associated with discrete glacial regions are comprised of different compound classes. Specifically, a larger proportion of protein-like compounds were observed in the supraglacial samples and in the early melt season (spring) subglacial discharge. In contrast, the late melt season (summer) subglacial discharge contained a greater fraction of lignin-like and other material presumably derived from underlying vegetation and soil. These results suggest (1) that the majority of supraglacial DOM originates from autochthonous microbial processes on the ice sheet surface, (2) that the subglacial DOM contains allochthonous carbon derived from overridden soils and vegetation as well as autochthonous carbon derived from in situ microbial metabolism, and (3) that the relative contribution of allochthonous and autochthonous material in subglacial discharge varies during the melt season. These conclusions are consistent with the hypothesis that, given sufficient time (e.g., overwinter storage), resident subglacial microbial communities may oxidize terrestrial material beneath the Greenland ice sheet.